[2026-05-29 22:17:18] [miniwdl-eks.task] Staging: downloading command and 2 inputs
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/67/67ee55803571d0d95b5d55b1eafca5a1/command /tmp/miniwdl_task/command
cp s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20251024_LH00519_0040_A235HV2LT4/dev-renasight_eb7639_251029121806/bams/3599981341_r4.bam.bai /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599981341_r4.bam.bai
cp s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20251024_LH00519_0040_A235HV2LT4/dev-renasight_eb7639_251029121806/bams/3599981341_r4.bam /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599981341_r4.bam
[2026-05-29 22:18:36] [miniwdl-eks.task] Staging completed (2 inputs, 77873ms) s5cmd=workers:256,concurrency:5,cpus:4
+ python /app/muc_finder.py /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599981341_r4.bam --output-vcf 3599981341_r4.bam.vcf
Loading wildtype catalog...
63 wildtype units loaded (0 skipped: [])
Sample: 3599981341_r4
BAM: /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599981341_r4.bam
[W::hts_idx_load3] The index file is older than the data file: /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599981341_r4.bam.bai
[W::hts_idx_load3] The index file is older than the data file: /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599981341_r4.bam.bai
Units: 4639 | Length-change anomalies: 30 | K-mer frac: 0.0070 | Call: POSITIVE
(K-mer rescued: kmer_frac=0.0070 >= 0.004)
Length-variant units:
Len Count Frac ED Match Description
---------------------------------------------------------------------------
61 11 0.0024 1 X +1bp ins at pos 21 (G), clinical: 59dupC
59 2 0.0004 19 D -1bp deletion (complex alignment)
59 2 0.0004 18 bJ -1bp deletion (complex alignment)
58 2 0.0004 22 aP -2bp deletion (complex alignment)
59 1 0.0002 18 P -1bp deletion (complex alignment)
59 1 0.0002 19 D -1bp deletion (complex alignment)
59 1 0.0002 18 D -1bp deletion (complex alignment)
62 1 0.0002 24 D +2bp insertion (complex alignment)
42 1 0.0002 19 W -18bp del at pos 35-52 (GCCCGGGGCCGGCCTGGT),
62 1 0.0002 24 D +2bp insertion (complex alignment)
42 1 0.0002 18 B -18bp del at pos 37-54 (CCGGGGCCGGCCTGCTCT),
18 1 0.0002 45 aN -42bp deletion (complex alignment)
59 1 0.0002 2 M -1bp deletion (complex alignment)
59 1 0.0002 21 D -1bp deletion (complex alignment)
61 1 0.0002 19 aE +1bp insertion (complex alignment)
Final call: POSITIVE
[]
K-mer evidence: kmer_frac=0.0070
[2026-05-29 22:18:36] [miniwdl-eks.task] Task finished exit_code=0 (557ms)
cp /tmp/miniwdl_task/stdout.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/67/67ee55803571d0d95b5d55b1eafca5a1/stdout.txt
cp /tmp/miniwdl_task/stderr.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/67/67ee55803571d0d95b5d55b1eafca5a1/stderr.txt
cp work/3599981341_r4.bam.vcf s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/67/67ee55803571d0d95b5d55b1eafca5a1/work/3599981341_r4.bam.vcf
cp work/_miniwdl_inputs/0/3599981341_r4.bam.bai s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/67/67ee55803571d0d95b5d55b1eafca5a1/work/_miniwdl_inputs/0/3599981341_r4.bam.bai
cp work/_miniwdl_inputs/0/3599981341_r4.bam s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/67/67ee55803571d0d95b5d55b1eafca5a1/work/_miniwdl_inputs/0/3599981341_r4.bam
cp /tmp/miniwdl_task/timing.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/67/67ee55803571d0d95b5d55b1eafca5a1/timing.json
cp /tmp/miniwdl_task/metrics.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/67/67ee55803571d0d95b5d55b1eafca5a1/metrics.json
cp /tmp/miniwdl_task/exit_code s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/67/67ee55803571d0d95b5d55b1eafca5a1/exit_code
[2026-05-29 22:20:04] [miniwdl-eks.task] Done exit_code=0 (87231ms unstage, 165662ms total)